So, about that presumed second DLC stage we might be getting, here are some conclusions I've made after a while of research.
-It will not be a bundle. Or, if it is a bundle, it will be a bundle that allows you to purchase a fighter and stage seperately. Our only example thusfar is Ryu. I will assume for the moment that the Newcomer+Stage model won't change (unless a newcomer lacks an accompanying stage.)
It will (probably) not be one of the following returning stages, as they have a number of themes present on other stages:
-Yoshi's Island (N64) ("Yoshi's Story" plays on Yoshi's Island (SSBM).)
-Mushroom Kingdom II ("Mushroom Kingdom II" was renamed "Ground Theme (Super Mario Bros. 2)", which is on Peach's Castle 64.)
-Rainbow Cruise (Both "Rainbow Cruise (Melee) and "Princess Peach's Castle" are on Delfino Plaza.)
-Princess Peach's Castle (See above.)
-Yoshi's Story ("Yoshi's Story Ver. 2" plays on Woolly World)
-Pokemon Stadium (All three themes from Brawl are present on Pokemon Stadium 2.)
-Poke Floats ("Poke Floats" is on Pokemon Stadium 2.)
-Green Greens ("Green Greens (Melee)" is on Great Cave Offensive.)
-Venom ("Venom" is on Lylat Cruise.)
-Fountain of Dreams ("Gourmet Race (Melee)" is on Dream Land 64.)
-Mute City ("Mute City (Remix)" is on Port Town Aero Dive, there's a new Mute City stage on the 3DS version, and we have 4 Mute City themes, yet no Melee Mute City.)
-Big Blue ("Big Blue" is on Port Town Aero Dive.)
-Brinstar Depths ("Brinstar Depths" is on Norfair.)
-Icicle Mountain ("Icicle Mountain (Melee)" is on Wrecking Crew, and... yeah, Ice Climbers are gone.)
-Kongo Jungle ("DK Rap" is on Jungle Hijinx.)
-New Pork City (Most of its music was ported to Onett and Magicant.)
-Frigate Orpheon (Every song except "Opening/Menu (Metroid Prime)" was ported to Pyrosphere.)
-Spear Pillar (Every song except the original composition of "Battle!" (Wild Pokemon (Diamond/Pearl) is present on other Pokemon stage.)
-Rumble Falls (All themes except "DK Jungle 1 Theme (Barrel Blast)" and "The Map Page/Bonus Level" have been scattered across DK stages.)
-Summit (All themes except the Brawl composition of "Balloon Trip" are on Dunk Hunt or Wrecking Crew.)
Plausible candidates:
Great Bay: Melee's composition of "Saria's Song" does not exist in this game. "Great Bay" was retitled "Main Theme (Legend of Zelda)". Additionally, there are a surprising lack of many Majora's Mask tracks in the game.
Fourside: "EarthBound" is not anywhere in Smash 4.
Planet Zebes : Track #8 has not appeared again in its original form. As we know from all 64 stages that have been ported since Melee, they do reuse the original tracks from the 64 version.
Saffron City: Track #12 has not appeared again in its original form.
Sector Z: Track #11 has not appeared again in its original form.
Special cases:
-Pirate Ship
Every song except the original composition of "The Great Sea" and "Molgera Battle" are present on other stages. This includes songs you'd expect to be on Pirate Ship, like "Song of Storms". Due to the absence of the "The Great Sea"'s not remix, it's not entirely impossible for this stage to pop up. I'd consider it very unlikely, though.
-Pictochat
Interestingly, a number of Pictochat songs are absent from the game. The main theme "Pictochat" is on "Pictochat 2 and "75m", so I doubt Pictochat's return, but this is worth a look.
Brawl's compositions of "Mii Channel" and "Wii Shop Channel" are absent. However, remixes of these themes are present elsewhere. Also absent from the game in any form that I'm aware of are "Charge! (Wii Play)" and "Shaberu! DS Cooking Navi".
This is probably as scattered as it was because Pictochat was one of the sole generic "Nintendo" stages in the game, a trait later split into numerous stages by the time Smash 4 came about. These stages tend to be dumping grounds for generic Nintendo-related stuff.
-Mario Bros:
"Gyromite" and "Mario Bros." are both present on retro-themed stages (Wrecking Crew and 75m) however, "Douchuumen (Nazo no Murasamejo)" , "Power-Up Music" and" the Brawl composition of "Famicom Medley" are absent. Due to the short length of the 8-bit "Mario Bros." theme and the remixed version being elsewhere, I'd file this under "unlikely".
-Mushroom Kingdom (Melee) and Mushroom Kingdom 64
Their main themes are the Super Mario Bros. theme, which will almost assuredly be on Super Mario Maker. I was surprised it already wasn't in the game.
It's also reasonable to guess that Snake would either be bundled with a new Metal Gear stage or Shadow Moses. I don't believe the second stage on the 30th will be Metal Gear related, and I don't believe the possible character we get will be Snake. Basically, Shadow Moses Island is also out of the picture in this circumstance.